April 2021
AIM: Given a reference sequence and a set of short reads, align each read to the reference sequence finding the most likely origin of the read sequence.
Aligners: STAR, HISAT2
Sequence Alignment/Map (SAM) format is the standard format for files containing aligned reads.
Definition of the format is available at https://samtools.github.io/hts-specs/SAMv1.pdf.
Two main parts:
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